Tractography question

[Indra Montserrat Fonseca Alfaro]

Hello! This is actually the first tractography I've been able to produce. I see that some tracts are missing (corpus callosum, front lobe, etc.) and that it doesn't look complete, but I don't know why. I used TrackVis, first using the default FACT and then I tried the second order Runge Kutta method, but both look weird to me. I tried masking with the b0 image but that didn't help at all. Does anyone have a suggestion/comment? 

These 3 are the FACT images: 

Runge Kutta: 

[Do Tromp]

Hi Indra, 

what you are seeing here is not bad, what is happening is that Trackvis has automatically applied a slice filter, and have skipping turned on to 99.9%, they did this to make it load quicker. I suggest turning those off and taking a second look. Looking at the images, I prefer the way the FACT looks better than the RK. 

If you haven't already, I'd suggest going though the tractography tutorial:

http://www.diffusion-imaging.com/2012/11/fiber-tracking-tutorial-step-by-step.html

Best of luck,

~Do